Workflow

Detailed software versions can be found under Rules.

Results

Workflow resultes
File Size Description Job properties
plot_jup_nb.html 295.1 kB
Job properties
Ruleplot_nb_2_html
plot_rmd_shell.html 1.5 MB
Job properties
Ruleplot_rmd_shell
plot_rmd_shell.png 962.9 kB
Job properties
Ruleplot_rmd_shell
plot_rmd_snakemake.html 1.5 MB
Job properties
Ruleplot_rmd_snakemake

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Configuration

Configuration files
File Code
config/config.yml 
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2
3
4
5
repo_version:
  "0.0.1"

dataset:
  "iris"

Rules

Workflow rules
Rule Jobs Output Singularity Conda environment Code
plot_rmd_snakemake 1
  • docs/html/plot_rmd_snakemake.html
 
source
plot_rmd_shell 1
  • docs/html/plot_rmd_shell.html
  • docs/png/plot_rmd_shell.png
 
1
R -e 'wd = getwd();                 rmarkdown::render( "{input[0]}",                     output_file = normalizePath( paste0( wd,"/" ,"{output[0]}" ) ),                     params = list(input = "{input[1]}",                                    output = "{output[1]}" ),                     knit_root_dir = getwd(),                     envir = new.env() )'
plot_nb_2_html 1
  • docs/html/plot_jup_nb.html
  • _libgcc_mutex=0.1=main
  • ansiwrap=0.8.4=py_0
  • arrow-cpp=0.13.0=py36h117bdfb_0
  • asn1crypto=1.2.0=py36_0
  • attrs=19.3.0=py_0
  • backcall=0.1.0=py36_0
  • backports=1.0=py_2
  • backports.tempfile=1.0=py_1
  • backports.weakref=1.0.post1=py_1
  • blas=1.0=mkl
  • bleach=3.1.0=py36_0
  • boost-cpp=1.67.0=h14c3975_4
  • brotli=1.0.7=he6710b0_0
  • bzip2=1.0.8=h7b6447c_0
  • ca-certificates=2019.11.28=hecc5488_0
  • certifi=2019.11.28=py36_0
  • cffi=1.13.2=py36h2e261b9_0
  • chardet=3.0.4=py36_1003
  • click=7.0=py36_0
  • cryptography=2.8=py36h1ba5d50_0
  • cycler=0.10.0=py36_0
  • dbus=1.13.12=h746ee38_0
  • decorator=4.4.1=py_0
  • defusedxml=0.6.0=py_0
  • double-conversion=3.1.5=he6710b0_1
  • entrypoints=0.3=py36_0
  • expat=2.2.6=he6710b0_0
  • feather-format=0.4.0=py_1003
  • fontconfig=2.13.0=h9420a91_0
  • freetype=2.9.1=h8a8886c_1
  • future=0.18.2=py36_0
  • gflags=2.2.2=he6710b0_0
  • glib=2.63.1=h5a9c865_0
  • glog=0.4.0=he6710b0_0
  • gmp=6.1.2=h6c8ec71_1
  • gst-plugins-base=1.14.0=hbbd80ab_1
  • gstreamer=1.14.0=hb453b48_1
  • icu=58.2=h9c2bf20_1
  • idna=2.8=py36_0
  • importlib_metadata=1.3.0=py36_0
  • intel-openmp=2019.4=243
  • ipykernel=5.1.3=py36h39e3cac_0
  • ipython=7.10.2=py36h39e3cac_0
  • ipython_genutils=0.2.0=py36_0
  • ipywidgets=7.5.1=py_0
  • jedi=0.15.1=py36_0
  • jinja2=2.10.3=py_0
  • jpeg=9b=h024ee3a_2
  • jsonschema=3.2.0=py36_0
  • jupyter=1.0.0=py36_7
  • jupyter_client=5.3.4=py36_0
  • jupyter_console=6.0.0=py36_0
  • jupyter_core=4.6.1=py36_0
  • kiwisolver=1.1.0=py36he6710b0_0
  • libboost=1.67.0=h46d08c1_4
  • libedit=3.1.20181209=hc058e9b_0
  • libevent=2.1.8=h1ba5d50_0
  • libffi=3.2.1=hd88cf55_4
  • libgcc-ng=9.1.0=hdf63c60_0
  • libgfortran-ng=7.3.0=hdf63c60_0
  • libpng=1.6.37=hbc83047_0
  • libprotobuf=3.6.0=hdbcaa40_0
  • libsodium=1.0.16=h1bed415_0
  • libstdcxx-ng=9.1.0=hdf63c60_0
  • libuuid=1.0.3=h1bed415_2
  • libxcb=1.13=h1bed415_1
  • libxml2=2.9.9=hea5a465_1
  • lz4-c=1.8.1.2=h14c3975_0
  • markupsafe=1.1.1=py36h7b6447c_0
  • matplotlib=3.1.1=py36h5429711_0
  • mistune=0.8.4=py36h7b6447c_0
  • mkl=2019.4=243
  • mkl-service=2.3.0=py36he904b0f_0
  • mkl_fft=1.0.15=py36ha843d7b_0
  • mkl_random=1.1.0=py36hd6b4f25_0
  • more-itertools=7.2.0=py36_0
  • nb_conda=2.2.1=py36_0
  • nb_conda_kernels=2.2.2=py36_0
  • nbconvert=5.6.1=py36_0
  • nbformat=4.4.0=py36_0
  • ncurses=6.1=he6710b0_1
  • notebook=6.0.2=py36_0
  • numpy=1.17.4=py36hc1035e2_0
  • numpy-base=1.17.4=py36hde5b4d6_0
  • openssl=1.1.1d=h516909a_0
  • pandas=0.25.3=py36he6710b0_0
  • pandoc=2.2.3.2=0
  • pandocfilters=1.4.2=py36_1
  • papermill=1.2.1=py36_0
  • parso=0.5.2=py_0
  • patsy=0.5.1=py36_0
  • pcre=8.43=he6710b0_0
  • pexpect=4.7.0=py36_0
  • pickleshare=0.7.5=py36_0
  • pip=19.3.1=py36_0
  • plotly=4.3.0=py_0
  • plotly_express=0.4.1=py_0
  • prometheus_client=0.7.1=py_0
  • prompt_toolkit=2.0.9=py36_0
  • ptyprocess=0.6.0=py36_0
  • pyaml=19.4.1=py_0
  • pyarrow=0.13.0=py36he6710b0_0
  • pycparser=2.19=py36_0
  • pygments=2.5.2=py_0
  • pyopenssl=19.1.0=py36_0
  • pyparsing=2.4.5=py_0
  • pyqt=5.9.2=py36h05f1152_2
  • pyrsistent=0.15.6=py36h7b6447c_0
  • pysocks=1.7.1=py36_0
  • python=3.6.9=h265db76_0
  • python-dateutil=2.8.1=py_0
  • pytz=2019.3=py_0
  • pyyaml=5.2=py36h7b6447c_0
  • pyzmq=18.1.0=py36he6710b0_0
  • qt=5.9.7=h5867ecd_1
  • qtconsole=4.6.0=py_0
  • re2=2019.08.01=he6710b0_0
  • readline=7.0=h7b6447c_5
  • requests=2.22.0=py36_1
  • retrying=1.3.3=py36_2
  • scipy=1.3.2=py36h7c811a0_0
  • seaborn=0.9.0=pyh91ea838_1
  • send2trash=1.5.0=py36_0
  • setuptools=42.0.2=py36_0
  • sip=4.19.8=py36hf484d3e_0
  • six=1.13.0=py36_0
  • snappy=1.1.7=hbae5bb6_3
  • sqlite=3.30.1=h7b6447c_0
  • statsmodels=0.10.1=py36hdd07704_0
  • tenacity=6.0.0=py36_0
  • terminado=0.8.3=py36_0
  • testpath=0.4.4=py_0
  • textwrap3=0.9.2=py_0
  • thrift-cpp=0.11.0=h02b749d_3
  • tk=8.6.8=hbc83047_0
  • tornado=6.0.3=py36h7b6447c_0
  • tqdm=4.40.2=py_0
  • traitlets=4.3.3=py36_0
  • urllib3=1.25.7=py36_0
  • wcwidth=0.1.7=py36_0
  • webencodings=0.5.1=py36_1
  • wheel=0.33.6=py36_0
  • widgetsnbextension=3.5.1=py36_0
  • xz=5.2.4=h14c3975_4
  • yaml=0.1.7=had09818_2
  • zeromq=4.3.1=he6710b0_3
  • zipp=0.6.0=py_0
  • zlib=1.2.11=h7b6447c_3
  • zstd=1.3.7=h0b5b093_0
  • {'pip': ['appdirs==1.4.3', 'configargparse==0.15.2', 'datrie==0.8', 'docutils==0.15.2', 'gitdb2==2.0.6', 'gitpython==3.0.5', 'psutil==5.6.7', 'ratelimiter==1.2.0.post0', 'smmap2==2.0.5', 'snakemake==5.8.2', 'wrapt==1.11.2']}
 
1
jupyter nbconvert --to html {input} --output ../../../{output}
load_dataset 1
  • data/out/feather/data.feather
  • _libgcc_mutex=0.1=main
  • ansiwrap=0.8.4=py_0
  • arrow-cpp=0.13.0=py36h117bdfb_0
  • asn1crypto=1.2.0=py36_0
  • attrs=19.3.0=py_0
  • backcall=0.1.0=py36_0
  • backports=1.0=py_2
  • backports.tempfile=1.0=py_1
  • backports.weakref=1.0.post1=py_1
  • blas=1.0=mkl
  • bleach=3.1.0=py36_0
  • boost-cpp=1.67.0=h14c3975_4
  • brotli=1.0.7=he6710b0_0
  • bzip2=1.0.8=h7b6447c_0
  • ca-certificates=2019.11.28=hecc5488_0
  • certifi=2019.11.28=py36_0
  • cffi=1.13.2=py36h2e261b9_0
  • chardet=3.0.4=py36_1003
  • click=7.0=py36_0
  • cryptography=2.8=py36h1ba5d50_0
  • cycler=0.10.0=py36_0
  • dbus=1.13.12=h746ee38_0
  • decorator=4.4.1=py_0
  • defusedxml=0.6.0=py_0
  • double-conversion=3.1.5=he6710b0_1
  • entrypoints=0.3=py36_0
  • expat=2.2.6=he6710b0_0
  • feather-format=0.4.0=py_1003
  • fontconfig=2.13.0=h9420a91_0
  • freetype=2.9.1=h8a8886c_1
  • future=0.18.2=py36_0
  • gflags=2.2.2=he6710b0_0
  • glib=2.63.1=h5a9c865_0
  • glog=0.4.0=he6710b0_0
  • gmp=6.1.2=h6c8ec71_1
  • gst-plugins-base=1.14.0=hbbd80ab_1
  • gstreamer=1.14.0=hb453b48_1
  • icu=58.2=h9c2bf20_1
  • idna=2.8=py36_0
  • importlib_metadata=1.3.0=py36_0
  • intel-openmp=2019.4=243
  • ipykernel=5.1.3=py36h39e3cac_0
  • ipython=7.10.2=py36h39e3cac_0
  • ipython_genutils=0.2.0=py36_0
  • ipywidgets=7.5.1=py_0
  • jedi=0.15.1=py36_0
  • jinja2=2.10.3=py_0
  • jpeg=9b=h024ee3a_2
  • jsonschema=3.2.0=py36_0
  • jupyter=1.0.0=py36_7
  • jupyter_client=5.3.4=py36_0
  • jupyter_console=6.0.0=py36_0
  • jupyter_core=4.6.1=py36_0
  • kiwisolver=1.1.0=py36he6710b0_0
  • libboost=1.67.0=h46d08c1_4
  • libedit=3.1.20181209=hc058e9b_0
  • libevent=2.1.8=h1ba5d50_0
  • libffi=3.2.1=hd88cf55_4
  • libgcc-ng=9.1.0=hdf63c60_0
  • libgfortran-ng=7.3.0=hdf63c60_0
  • libpng=1.6.37=hbc83047_0
  • libprotobuf=3.6.0=hdbcaa40_0
  • libsodium=1.0.16=h1bed415_0
  • libstdcxx-ng=9.1.0=hdf63c60_0
  • libuuid=1.0.3=h1bed415_2
  • libxcb=1.13=h1bed415_1
  • libxml2=2.9.9=hea5a465_1
  • lz4-c=1.8.1.2=h14c3975_0
  • markupsafe=1.1.1=py36h7b6447c_0
  • matplotlib=3.1.1=py36h5429711_0
  • mistune=0.8.4=py36h7b6447c_0
  • mkl=2019.4=243
  • mkl-service=2.3.0=py36he904b0f_0
  • mkl_fft=1.0.15=py36ha843d7b_0
  • mkl_random=1.1.0=py36hd6b4f25_0
  • more-itertools=7.2.0=py36_0
  • nb_conda=2.2.1=py36_0
  • nb_conda_kernels=2.2.2=py36_0
  • nbconvert=5.6.1=py36_0
  • nbformat=4.4.0=py36_0
  • ncurses=6.1=he6710b0_1
  • notebook=6.0.2=py36_0
  • numpy=1.17.4=py36hc1035e2_0
  • numpy-base=1.17.4=py36hde5b4d6_0
  • openssl=1.1.1d=h516909a_0
  • pandas=0.25.3=py36he6710b0_0
  • pandoc=2.2.3.2=0
  • pandocfilters=1.4.2=py36_1
  • papermill=1.2.1=py36_0
  • parso=0.5.2=py_0
  • patsy=0.5.1=py36_0
  • pcre=8.43=he6710b0_0
  • pexpect=4.7.0=py36_0
  • pickleshare=0.7.5=py36_0
  • pip=19.3.1=py36_0
  • plotly=4.3.0=py_0
  • plotly_express=0.4.1=py_0
  • prometheus_client=0.7.1=py_0
  • prompt_toolkit=2.0.9=py36_0
  • ptyprocess=0.6.0=py36_0
  • pyaml=19.4.1=py_0
  • pyarrow=0.13.0=py36he6710b0_0
  • pycparser=2.19=py36_0
  • pygments=2.5.2=py_0
  • pyopenssl=19.1.0=py36_0
  • pyparsing=2.4.5=py_0
  • pyqt=5.9.2=py36h05f1152_2
  • pyrsistent=0.15.6=py36h7b6447c_0
  • pysocks=1.7.1=py36_0
  • python=3.6.9=h265db76_0
  • python-dateutil=2.8.1=py_0
  • pytz=2019.3=py_0
  • pyyaml=5.2=py36h7b6447c_0
  • pyzmq=18.1.0=py36he6710b0_0
  • qt=5.9.7=h5867ecd_1
  • qtconsole=4.6.0=py_0
  • re2=2019.08.01=he6710b0_0
  • readline=7.0=h7b6447c_5
  • requests=2.22.0=py36_1
  • retrying=1.3.3=py36_2
  • scipy=1.3.2=py36h7c811a0_0
  • seaborn=0.9.0=pyh91ea838_1
  • send2trash=1.5.0=py36_0
  • setuptools=42.0.2=py36_0
  • sip=4.19.8=py36hf484d3e_0
  • six=1.13.0=py36_0
  • snappy=1.1.7=hbae5bb6_3
  • sqlite=3.30.1=h7b6447c_0
  • statsmodels=0.10.1=py36hdd07704_0
  • tenacity=6.0.0=py36_0
  • terminado=0.8.3=py36_0
  • testpath=0.4.4=py_0
  • textwrap3=0.9.2=py_0
  • thrift-cpp=0.11.0=h02b749d_3
  • tk=8.6.8=hbc83047_0
  • tornado=6.0.3=py36h7b6447c_0
  • tqdm=4.40.2=py_0
  • traitlets=4.3.3=py36_0
  • urllib3=1.25.7=py36_0
  • wcwidth=0.1.7=py36_0
  • webencodings=0.5.1=py36_1
  • wheel=0.33.6=py36_0
  • widgetsnbextension=3.5.1=py36_0
  • xz=5.2.4=h14c3975_4
  • yaml=0.1.7=had09818_2
  • zeromq=4.3.1=he6710b0_3
  • zipp=0.6.0=py_0
  • zlib=1.2.11=h7b6447c_3
  • zstd=1.3.7=h0b5b093_0
  • {'pip': ['appdirs==1.4.3', 'configargparse==0.15.2', 'datrie==0.8', 'docutils==0.15.2', 'gitdb2==2.0.6', 'gitpython==3.0.5', 'psutil==5.6.7', 'ratelimiter==1.2.0.post0', 'smmap2==2.0.5', 'snakemake==5.8.2', 'wrapt==1.11.2']}
 
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 3
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 5
 6
 7
 8
 9
10
import seaborn as sns
import pandas as pd

params = snakemake.config

df = sns.load_dataset(params['dataset'])

df.to_feather(snakemake.output[0])

print('load finished')
plot_execute_nb_plot 1
  • src/nb/executed/plot.ipynb
  • _libgcc_mutex=0.1=main
  • ansiwrap=0.8.4=py_0
  • arrow-cpp=0.13.0=py36h117bdfb_0
  • asn1crypto=1.2.0=py36_0
  • attrs=19.3.0=py_0
  • backcall=0.1.0=py36_0
  • backports=1.0=py_2
  • backports.tempfile=1.0=py_1
  • backports.weakref=1.0.post1=py_1
  • blas=1.0=mkl
  • bleach=3.1.0=py36_0
  • boost-cpp=1.67.0=h14c3975_4
  • brotli=1.0.7=he6710b0_0
  • bzip2=1.0.8=h7b6447c_0
  • ca-certificates=2019.11.28=hecc5488_0
  • certifi=2019.11.28=py36_0
  • cffi=1.13.2=py36h2e261b9_0
  • chardet=3.0.4=py36_1003
  • click=7.0=py36_0
  • cryptography=2.8=py36h1ba5d50_0
  • cycler=0.10.0=py36_0
  • dbus=1.13.12=h746ee38_0
  • decorator=4.4.1=py_0
  • defusedxml=0.6.0=py_0
  • double-conversion=3.1.5=he6710b0_1
  • entrypoints=0.3=py36_0
  • expat=2.2.6=he6710b0_0
  • feather-format=0.4.0=py_1003
  • fontconfig=2.13.0=h9420a91_0
  • freetype=2.9.1=h8a8886c_1
  • future=0.18.2=py36_0
  • gflags=2.2.2=he6710b0_0
  • glib=2.63.1=h5a9c865_0
  • glog=0.4.0=he6710b0_0
  • gmp=6.1.2=h6c8ec71_1
  • gst-plugins-base=1.14.0=hbbd80ab_1
  • gstreamer=1.14.0=hb453b48_1
  • icu=58.2=h9c2bf20_1
  • idna=2.8=py36_0
  • importlib_metadata=1.3.0=py36_0
  • intel-openmp=2019.4=243
  • ipykernel=5.1.3=py36h39e3cac_0
  • ipython=7.10.2=py36h39e3cac_0
  • ipython_genutils=0.2.0=py36_0
  • ipywidgets=7.5.1=py_0
  • jedi=0.15.1=py36_0
  • jinja2=2.10.3=py_0
  • jpeg=9b=h024ee3a_2
  • jsonschema=3.2.0=py36_0
  • jupyter=1.0.0=py36_7
  • jupyter_client=5.3.4=py36_0
  • jupyter_console=6.0.0=py36_0
  • jupyter_core=4.6.1=py36_0
  • kiwisolver=1.1.0=py36he6710b0_0
  • libboost=1.67.0=h46d08c1_4
  • libedit=3.1.20181209=hc058e9b_0
  • libevent=2.1.8=h1ba5d50_0
  • libffi=3.2.1=hd88cf55_4
  • libgcc-ng=9.1.0=hdf63c60_0
  • libgfortran-ng=7.3.0=hdf63c60_0
  • libpng=1.6.37=hbc83047_0
  • libprotobuf=3.6.0=hdbcaa40_0
  • libsodium=1.0.16=h1bed415_0
  • libstdcxx-ng=9.1.0=hdf63c60_0
  • libuuid=1.0.3=h1bed415_2
  • libxcb=1.13=h1bed415_1
  • libxml2=2.9.9=hea5a465_1
  • lz4-c=1.8.1.2=h14c3975_0
  • markupsafe=1.1.1=py36h7b6447c_0
  • matplotlib=3.1.1=py36h5429711_0
  • mistune=0.8.4=py36h7b6447c_0
  • mkl=2019.4=243
  • mkl-service=2.3.0=py36he904b0f_0
  • mkl_fft=1.0.15=py36ha843d7b_0
  • mkl_random=1.1.0=py36hd6b4f25_0
  • more-itertools=7.2.0=py36_0
  • nb_conda=2.2.1=py36_0
  • nb_conda_kernels=2.2.2=py36_0
  • nbconvert=5.6.1=py36_0
  • nbformat=4.4.0=py36_0
  • ncurses=6.1=he6710b0_1
  • notebook=6.0.2=py36_0
  • numpy=1.17.4=py36hc1035e2_0
  • numpy-base=1.17.4=py36hde5b4d6_0
  • openssl=1.1.1d=h516909a_0
  • pandas=0.25.3=py36he6710b0_0
  • pandoc=2.2.3.2=0
  • pandocfilters=1.4.2=py36_1
  • papermill=1.2.1=py36_0
  • parso=0.5.2=py_0
  • patsy=0.5.1=py36_0
  • pcre=8.43=he6710b0_0
  • pexpect=4.7.0=py36_0
  • pickleshare=0.7.5=py36_0
  • pip=19.3.1=py36_0
  • plotly=4.3.0=py_0
  • plotly_express=0.4.1=py_0
  • prometheus_client=0.7.1=py_0
  • prompt_toolkit=2.0.9=py36_0
  • ptyprocess=0.6.0=py36_0
  • pyaml=19.4.1=py_0
  • pyarrow=0.13.0=py36he6710b0_0
  • pycparser=2.19=py36_0
  • pygments=2.5.2=py_0
  • pyopenssl=19.1.0=py36_0
  • pyparsing=2.4.5=py_0
  • pyqt=5.9.2=py36h05f1152_2
  • pyrsistent=0.15.6=py36h7b6447c_0
  • pysocks=1.7.1=py36_0
  • python=3.6.9=h265db76_0
  • python-dateutil=2.8.1=py_0
  • pytz=2019.3=py_0
  • pyyaml=5.2=py36h7b6447c_0
  • pyzmq=18.1.0=py36he6710b0_0
  • qt=5.9.7=h5867ecd_1
  • qtconsole=4.6.0=py_0
  • re2=2019.08.01=he6710b0_0
  • readline=7.0=h7b6447c_5
  • requests=2.22.0=py36_1
  • retrying=1.3.3=py36_2
  • scipy=1.3.2=py36h7c811a0_0
  • seaborn=0.9.0=pyh91ea838_1
  • send2trash=1.5.0=py36_0
  • setuptools=42.0.2=py36_0
  • sip=4.19.8=py36hf484d3e_0
  • six=1.13.0=py36_0
  • snappy=1.1.7=hbae5bb6_3
  • sqlite=3.30.1=h7b6447c_0
  • statsmodels=0.10.1=py36hdd07704_0
  • tenacity=6.0.0=py36_0
  • terminado=0.8.3=py36_0
  • testpath=0.4.4=py_0
  • textwrap3=0.9.2=py_0
  • thrift-cpp=0.11.0=h02b749d_3
  • tk=8.6.8=hbc83047_0
  • tornado=6.0.3=py36h7b6447c_0
  • tqdm=4.40.2=py_0
  • traitlets=4.3.3=py36_0
  • urllib3=1.25.7=py36_0
  • wcwidth=0.1.7=py36_0
  • webencodings=0.5.1=py36_1
  • wheel=0.33.6=py36_0
  • widgetsnbextension=3.5.1=py36_0
  • xz=5.2.4=h14c3975_4
  • yaml=0.1.7=had09818_2
  • zeromq=4.3.1=he6710b0_3
  • zipp=0.6.0=py_0
  • zlib=1.2.11=h7b6447c_3
  • zstd=1.3.7=h0b5b093_0
  • {'pip': ['appdirs==1.4.3', 'configargparse==0.15.2', 'datrie==0.8', 'docutils==0.15.2', 'gitdb2==2.0.6', 'gitpython==3.0.5', 'psutil==5.6.7', 'ratelimiter==1.2.0.post0', 'smmap2==2.0.5', 'snakemake==5.8.2', 'wrapt==1.11.2']}
 
1
python -c 'import papermill as pm;             pm.execute_notebook(  "{input[0]}"                     , "{output[0]}"                     , parameters = dict( input = "{input[1]}") )'